[2023-03-15 13:03:53,431] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:53,431] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:53,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e73b9f7-bd63-4ec5-9f47-5cdafdea9ae6/dqc_reference
[2023-03-15 13:03:54,595] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:54,596] [INFO] Task started: Prodigal
[2023-03-15 13:03:54,596] [INFO] Running command: cat /var/lib/cwl/stg1f48af9a-c0b8-4fb7-b345-83bcac75026f/OceanDNA-b25966.fa | prodigal -d OceanDNA-b25966/cds.fna -a OceanDNA-b25966/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:01,878] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:01,878] [INFO] Task started: HMMsearch
[2023-03-15 13:04:01,878] [INFO] Running command: hmmsearch --tblout OceanDNA-b25966/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e73b9f7-bd63-4ec5-9f47-5cdafdea9ae6/dqc_reference/reference_markers.hmm OceanDNA-b25966/protein.faa > /dev/null
[2023-03-15 13:04:02,149] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:02,150] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1f48af9a-c0b8-4fb7-b345-83bcac75026f/OceanDNA-b25966.fa]
[2023-03-15 13:04:02,165] [INFO] Query marker FASTA was written to OceanDNA-b25966/markers.fasta
[2023-03-15 13:04:02,165] [INFO] Task started: Blastn
[2023-03-15 13:04:02,165] [INFO] Running command: blastn -query OceanDNA-b25966/markers.fasta -db /var/lib/cwl/stg8e73b9f7-bd63-4ec5-9f47-5cdafdea9ae6/dqc_reference/reference_markers.fasta -out OceanDNA-b25966/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:02,728] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:02,729] [INFO] Selected 17 target genomes.
[2023-03-15 13:04:02,729] [INFO] Target genome list was writen to OceanDNA-b25966/target_genomes.txt
[2023-03-15 13:04:02,739] [INFO] Task started: fastANI
[2023-03-15 13:04:02,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f48af9a-c0b8-4fb7-b345-83bcac75026f/OceanDNA-b25966.fa --refList OceanDNA-b25966/target_genomes.txt --output OceanDNA-b25966/fastani_result.tsv --threads 1
[2023-03-15 13:04:09,667] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:09,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e73b9f7-bd63-4ec5-9f47-5cdafdea9ae6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:09,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e73b9f7-bd63-4ec5-9f47-5cdafdea9ae6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:09,668] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:04:09,668] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:04:09,668] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-15 13:04:09,668] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25966/tc_result.tsv
[2023-03-15 13:04:09,668] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:09,669] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:09,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e73b9f7-bd63-4ec5-9f47-5cdafdea9ae6/dqc_reference/checkm_data
[2023-03-15 13:04:09,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:09,675] [INFO] Task started: CheckM
[2023-03-15 13:04:09,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25966/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25966/checkm_input OceanDNA-b25966/checkm_result
[2023-03-15 13:04:33,264] [INFO] Task succeeded: CheckM
[2023-03-15 13:04:33,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:04:33,267] [INFO] ===== Completeness check finished =====
[2023-03-15 13:04:33,267] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:04:33,267] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25966/markers.fasta)
[2023-03-15 13:04:33,267] [INFO] Task started: Blastn
[2023-03-15 13:04:33,267] [INFO] Running command: blastn -query OceanDNA-b25966/markers.fasta -db /var/lib/cwl/stg8e73b9f7-bd63-4ec5-9f47-5cdafdea9ae6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25966/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:34,075] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:34,076] [INFO] Selected 21 target genomes.
[2023-03-15 13:04:34,076] [INFO] Target genome list was writen to OceanDNA-b25966/target_genomes_gtdb.txt
[2023-03-15 13:04:34,156] [INFO] Task started: fastANI
[2023-03-15 13:04:34,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f48af9a-c0b8-4fb7-b345-83bcac75026f/OceanDNA-b25966.fa --refList OceanDNA-b25966/target_genomes_gtdb.txt --output OceanDNA-b25966/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:04:40,390] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:40,401] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:04:40,401] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_905182395.1	s__CAJJBL01 sp905182395	99.1909	344	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__CAJJBL01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016777705.1	s__AAA536-G10 sp016777705	77.16	142	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	96.71	95.13	0.61	0.57	3	-
GCA_902528415.1	s__AAA536-G10 sp902528415	76.9658	106	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	95.26	95.26	0.64	0.64	2	-
GCA_902619805.1	s__AAA536-G10 sp902619805	76.9492	135	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000421325.1	s__AAA536-G10 sp000421325	76.9287	133	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517275.1	s__AAA536-G10 sp902517275	76.8741	83	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558885.1	s__AAA536-G10 sp902558885	76.7754	123	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902529515.1	s__AAA536-G10 sp902529515	76.7086	91	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.18	97.18	0.52	0.52	2	-
GCA_902593735.1	s__AAA536-G10 sp902593735	76.7031	113	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902583415.1	s__AAA536-G10 sp902583415	76.6923	98	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384615.1	s__AAA536-G10 sp000384615	76.6655	136	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592615.1	s__AAA536-G10 sp902592615	76.6621	114	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282145.1	s__AAA536-G10 sp003282145	76.651	140	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902619615.1	s__AAA536-G10 sp902619615	76.63	145	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777645.1	s__AAA536-G10 sp016777645	76.5846	96	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625215.1	s__AAA536-G10 sp902625215	76.4648	128	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622875.1	s__AAA536-G10 sp902622875	76.4397	133	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282435.1	s__AAA536-G10 sp003282435	76.4382	88	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595145.1	s__AAA536-G10 sp902595145	76.3379	119	486	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:04:40,402] [INFO] GTDB search result was written to OceanDNA-b25966/result_gtdb.tsv
[2023-03-15 13:04:40,402] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:04:40,403] [INFO] DFAST_QC result json was written to OceanDNA-b25966/dqc_result.json
[2023-03-15 13:04:40,403] [INFO] DFAST_QC completed!
[2023-03-15 13:04:40,403] [INFO] Total running time: 0h0m47s